Fix lost logcontext when using `timeout_deferred(...)` and things
actually timeout.
Fix https://github.com/element-hq/synapse/issues/19087 (our HTTP client
times out requests using `timeout_deferred(...)`
Fix https://github.com/element-hq/synapse/issues/19066 (`/sync` uses
`notifier.wait_for_events()` which uses `timeout_deferred(...)` under
the hood)
### When/why did these lost logcontext warnings start happening?
```
synapse.logging.context - 107 - WARNING - sentinel - Expected logging context call_later but found POST-2453
synapse.logging.context - 107 - WARNING - sentinel - Expected logging context call_later was lost
```
In https://github.com/element-hq/synapse/pull/18828, we switched
`timeout_deferred(...)` from using `reactor.callLater(...)` to
[`clock.call_later(...)`](3b59ac3b69/synapse/util/clock.py (L224-L313))
under the hood. This meant it started dealing with logcontexts but our
`time_it_out()` callback didn't follow our [Synapse logcontext
rules](3b59ac3b69/docs/log_contexts.md).